The process of resonance capture has been well studied for planetary systems where the potential is generated exclusively by the star. However, massive protoplanetary disks add a significant perturbation to these models. In this paper we examine the role of a protoplanetary disk’s gravitational potential in shaping the structure of mean motion resonances in the planetary system. The disk induces precession and changes the mean motion of nearby planets which causes resonances to split and shift from their unperturbed locations. As the disk evaporates these resonances merge and interact. We understand these effects with a combination of semi-analytic models and numerical integration, both of resonance capture under the combined potential of the star and disk and of the disk’s subsequent dispersal. These interactions result in complicated dynamical behaviors that may have observational consequences for interpreting the population of exoplanets.